sam
What is a .sam file?
text/x-sam
SAM (Sequence Alignment/Map) is the plain-text format for sequence alignments and the human-readable counterpart of binary BAM. An optional header of `@`-prefixed lines declares the sort order and reference sequences, and each alignment line has eleven mandatory tab-separated fields — including a bitwise FLAG, a 1-based position, a CIGAR string describing the match, and the sequence and its qualities — followed by optional typed TAG:TYPE:VALUE fields.
How to use a .sam file
Use an example .sam file to test alignment parsers and format converters, exercising FLAG bit decoding, CIGAR operations that consume the reference but not the read, and the difference between unmapped records and records on an absent reference.